8. Species
==================

-----------
8.1 Ensembl
-----------
The promoter region of any Ensembl transcript of any species within any column can be compared against the other members of the same column in order to identify a conserved binding site of the 575 transcription factors described in the Jaspar database.  The Enredo-Pecan-Ortheus pipeline was used to create whole genome alignments between the species in each column.  'EPO_LOW' indicates this column also contains genomes for which the sequencing of the current version is still considered low-coverage.  The TFBS footprinting pipeline partially accounts for this by removing sequences from alignments which appear to be missing segments.  Due to the significantly greater number of species, we recommend using the low coverage versions except for primate comparisons which do not have a low coverage version.

View the available Ensembl species groups to plan your analysis: https://rest.ensembl.org/info/compara/species_sets/EPO_LOW_COVERAGE?content-type=application/json.

-----------------
8.2 Species table
-----------------
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|EPO_LOW mammals           |EPO_LOW fish          |EPO_LOW sauropsids |EPO mammals          |EPO primates       |EPO fish              |EPO sauropsids     |
+==========================+======================+===================+=====================+===================+======================+===================+
|ailuropoda_melanoleuca    |astyanax_mexicanus    |anas_platyrhynchos |bos_taurus           |callithrix_jacchus |danio_rerio           |anolis_carolinensis|
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|bos_taurus                |danio_rerio           |anolis_carolinensis|callithrix_jacchus   |chlorocebus_sabaeus|gasterosteus_aculeatus|gallus_gallus      |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|callithrix_jacchus        |gadus_morhua          |ficedula_albicollis|canis_familiaris     |gorilla_gorilla    |lepisosteus_oculatus  |meleagris_gallopavo|
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|canis_familiaris          |gasterosteus_aculeatus|gallus_gallus      |chlorocebus_sabaeus  |homo_sapiens       |oryzias_latipes       |taeniopygia_guttata|
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|cavia_porcellus           |lepisosteus_oculatus  |meleagris_gallopavo|equus_caballus       |macaca_mulatta     |tetraodon_nigroviridis|                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|chlorocebus_sabaeus       |oreochromis_niloticus |pelodiscus_sinensis|felis_catus          |pan_troglodytes    |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|choloepus_hoffmanni       |oryzias_latipes       |taeniopygia_guttata|gorilla_gorilla      |papio_anubis       |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|dasypus_novemcinctus      |poecilia_formosa      |                   |homo_sapiens         |pongo_abelii       |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|dipodomys_ordii           |takifugu_rubripes     |                   |macaca_mulatta       |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|echinops_telfairi         |tetraodon_nigroviridis|                   |mus_musculus         |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|equus_caballus            |xiphophorus_maculatus |                   |oryctolagus_cuniculus|                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|erinaceus_europaeus       |                      |                   |ovis_aries           |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|felis_catus               |                      |                   |pan_troglodytes      |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|gorilla_gorilla           |                      |                   |papio_anubis         |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|homo_sapiens              |                      |                   |pongo_abelii         |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|ictidomys_tridecemlineatus|                      |                   |rattus_norvegicus    |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|loxodonta_africana        |                      |                   |sus_scrofa           |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|macaca_mulatta            |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|microcebus_murinus        |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|mus_musculus              |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|mustela_putorius_furo     |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|myotis_lucifugus          |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|nomascus_leucogenys       |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|ochotona_princeps         |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|oryctolagus_cuniculus     |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|otolemur_garnettii        |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|ovis_aries                |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|pan_troglodytes           |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|papio_anubis              |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|pongo_abelii              |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|procavia_capensis         |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|pteropus_vampyrus         |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|rattus_norvegicus         |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|sorex_araneus             |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|sus_scrofa                |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|tarsius_syrichta          |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|tupaia_belangeri          |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|tursiops_truncatus        |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+
|vicugna_pacos             |                      |                   |                     |                   |                      |                   |
+--------------------------+----------------------+-------------------+---------------------+-------------------+----------------------+-------------------+